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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttactatactgaattagtttaaaccattgagttcctttgaatcgaaaagacgaaactgctgtgcatgttttgttccttctgatctgttctttcaca...

Basic information

species Oryza sativa
transcript LOC_Os01g38620.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g38620.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G142984_T01 (Zea mays), 5'ss of exon 5
ATCGCTTATTCTCTGTTAGA------GGAGCAGGAAGGGAAAAAGAGAGGATACGATGAGTACA------TATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttactatactgaattagtttaaaccat-tgagttcctttgaatcgaaaagacgaaactgctgtgcatgttttgttccttctgatctgttctttcaca--
|||||| |||| |||||||||||| ||||||| || ||||| |||| |||||||||||||||| ||||||||| ||||| ||||||| ||||||||| || | | | || || |||| ||| | | | | ||| | | | | | ||||
---------TCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACATCTGATGATTACAATTACATATCTTTTGTCAGCCTTCTTGCTGATAAACGATACTGTGgtatgtactatact---ccgattcgagctgtatgccttttcatgaaaggaacatatatagtgcaaccatacagattggtgcaaccatgcagccaagacacaaa
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|218487804|gb|FG952787.1|FG952787
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|58594793|gb|CF993101.1|CF993101
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTA
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTA
EST: gi|27577389|gb|CB000084.1|CB000084
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|218504651|gb|FG960768.1|FG960768
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|33795398|gb|CF323569.1|CF323569
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|58655403|gb|CK044083.1|CK044083
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|38472674|gb|CF956806.1|CF956806
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|86908033|gb|CI298799.1|CI298799
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|27577966|gb|CB000661.1|CB000661
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAA
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAA
EST: gi|218495275|gb|FG966279.1|FG966279
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|218500721|gb|FG955417.1|FG955417
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|33793613|gb|CF322690.1|CF322690
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|38478638|gb|CF962771.1|CF962771
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGA
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGA
EST: gi|58588638|gb|CF986946.1|CF986946
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGG
EST: gi|27577933|gb|CB000628.1|CB000628
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|58598824|gb|CK009352.1|CK009352
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|218483500|gb|FG948234.1|FG948234
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAACAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|25801465|gb|CA757426.1|CA757426
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGA
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGA
EST: gi|218502513|gb|FG958404.1|FG958404
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTA
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTA
EST: gi|218499923|gb|FG954899.1|FG954899
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttactatactgaattagtttaaaccattgagttcctttgaatcgaaaagacgaaactgctgtgcatgttttgttccttctgatctgttctttcaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT